diff --git a/refresh.template.py b/refresh.template.py
index 6604621..e028c99 100644
--- a/refresh.template.py
+++ b/refresh.template.py
@@ -89,6 +89,35 @@ def _print_header_finding_warning_once():
 _print_header_finding_warning_once.has_logged = False
 
 
+@functools.lru_cache
+def _get_bazel_version():
+    """Gets the Bazel version as a tuple of (major, minor, patch).
+
+    The rolling release and the release candidate are treated as the LTS release.
+    E.g. both 7.0.0-pre.XXXXXXXX.X and 7.0.0rc1 are treated as 7.0.0.
+    If the version can't be determined, returns (0, 0, 0).
+    """
+    bazel_version_process = subprocess.run(
+        ['bazel', 'version'],
+        capture_output=True,
+        encoding=locale.getpreferredencoding(),
+        check=True, # Should always succeed.
+    )
+
+    version = ''
+    for line in bazel_version_process.stdout.splitlines():
+        line = line.strip()
+        if line.startswith('Build label: '):
+            version = line[len('Build label: '):]
+
+    match = re.search(r'^(\d+)\.(\d+)\.(\d+)', version)
+    if not match:
+        log_warning(f">>> Failed to get Bazel version.\nPlease file an issue with the following log:\n", bazel_version_process.stdout)
+        return (0, 0, 0)
+
+    return tuple(int(match.group(i)) for i in range(1, 4))
+
+
 @functools.lru_cache
 def _get_bazel_cached_action_keys():
     """Gets the set of actionKeys cached in bazel-out."""
@@ -727,6 +756,19 @@ def _apple_platform_patch(compile_args: list[str]):
     return compile_args
 
 
+def _get_sysroot(args: typing.List[str]):
+    """Get path to sysroot from command line arguments."""
+    for idx, arg in enumerate(args):
+        if arg == '--sysroot' or arg == '-isysroot':
+            if idx + 1 < len(args):
+                return pathlib.PurePath(args[idx + 1])
+        elif arg.startswith('--sysroot='):
+            return pathlib.PurePath(arg[len('--sysroot='):])
+        elif arg.startswith('-isysroot'):
+            return pathlib.PurePath(arg[len('-isysroot'):])
+    return None
+
+
 def _emscripten_platform_patch(compile_action):
     """De-Bazel the command into something clangd can parse.
 
@@ -737,6 +779,13 @@ def _emscripten_platform_patch(compile_action):
         return compile_action.arguments
 
     workspace_absolute = pathlib.PurePath(os.environ["BUILD_WORKSPACE_DIRECTORY"])
+    sysroot = _get_sysroot(compile_action.arguments)
+    assert sysroot, f'Emscripten sysroot not detected in CMD: {compile_action.arguments}'
+
+    def get_workspace_root(path_from_execroot: pathlib.PurePath):
+        if path_from_execroot.parts[0] != 'external':
+            return pathlib.PurePath('.')
+        return pathlib.PurePath('external') / path_from_execroot.parts[1]
 
     environment = compile_action.environmentVariables.copy()
     environment['EXT_BUILD_ROOT'] = str(workspace_absolute)
@@ -744,6 +793,10 @@ def _emscripten_platform_patch(compile_action):
     environment['EM_COMPILER_WRAPPER'] = str(pathlib.PurePath({print_args_executable}))
     if 'PATH' not in environment:
         environment['PATH'] = os.environ['PATH']
+    if 'EM_BIN_PATH' not in environment:
+        environment['EM_BIN_PATH'] = str(get_workspace_root(sysroot))
+    if 'EM_CONFIG_PATH' not in environment:
+        environment['EM_CONFIG_PATH'] = str(get_workspace_root(emcc_driver) / 'emscripten_toolchain' / 'emscripten_config')
 
     # We run the emcc process with the environment variable EM_COMPILER_WRAPPER to intercept the command line arguments passed to `clang`.
     emcc_process = subprocess.run(
@@ -1143,13 +1196,17 @@ def _get_commands(target: str, flags: str):
         # That's all well and good, but param files would prevent us from seeing compile actions before the param files had been generated by compilation.
         # Since clangd has no such length limit, we'll disable param files for our aquery run.
         '--features=-compiler_param_file',
-        '--host_features=-compiler_param_file',
         # Disable layering_check during, because it causes large-scale dependence on generated module map files that prevent header extraction before their generation
             # For more context, see https://github.com/hedronvision/bazel-compile-commands-extractor/issues/83
             # If https://github.com/clangd/clangd/issues/123 is resolved and we're not doing header extraction, we could try removing this, checking that there aren't erroneous red squigglies squigglies before the module maps are generated.
             # If Bazel starts supporting modules (https://github.com/bazelbuild/bazel/issues/4005), we'll probably need to make changes that subsume this.
         '--features=-layering_check',
-    ] + additional_flags
+    ]
+
+    if _get_bazel_version() >= (6, 1, 0):
+        aquery_args += ['--host_features=-compiler_param_file']
+
+    aquery_args += additional_flags
 
     aquery_process = subprocess.run(
         aquery_args,
diff --git a/refresh_compile_commands.bzl b/refresh_compile_commands.bzl
index 5ce7461..5231721 100644
--- a/refresh_compile_commands.bzl
+++ b/refresh_compile_commands.bzl
@@ -82,7 +82,7 @@ def refresh_compile_commands(
 
     # Make any package-relative labels absolute
     targets = {
-        target if target.startswith("/") or target.startswith("@") else "@{}//{}:{}".format(native.repository_name(), native.package_name(), target.removeprefix(":")): flags for target, flags in targets.items()
+        target if target.startswith("/") or target.startswith("@") else "{}//{}:{}".format(native.repository_name(), native.package_name(), target.removeprefix(":")): flags for target, flags in targets.items()
     }
 
     # Generate the core, runnable python script from refresh.template.py